rs207524

Variant names:

• chr21-23814172-C-A
• rs207524
• ENST00000807614.1:n.123+1435C>A

Your query was ambiguous. Multiple possible variants found:

• chr21-23814172-C-A
• chr21-23814172-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000807614.1(ENSG00000287612):​n.123+1435C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.972 in 151,630 control chromosomes in the GnomAD database, including 71,582 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.97 (71582 hom., cov: 31)
• Consequence: ENSG00000287612 ENST00000807614.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 2 publications found

Genes affected

ENSG00000287612 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372750	XR_937612.2	n.121+1435C>A		intron_variant	Intron 1 of 4
LOC105372750	XR_937613.2	n.121+1435C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287612	ENST00000807614.1	n.123+1435C>A		intron_variant	Intron 1 of 3
ENSG00000287612	ENST00000807615.1	n.126+1435C>A		intron_variant	Intron 1 of 2
ENSG00000287612	ENST00000807616.1	n.88+1435C>A		intron_variant	Intron 1 of 2
ENSG00000287612	ENST00000807617.1	n.98+1435C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.972 AC: 147296 AN: 151514 Hom.: 71539 Cov.: 31

Gnomad AFR AF: 0.905

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.988

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.978

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.972 AC: 147397 AN: 151630 Hom.: 71582 Cov.: 31 AF XY: 0.973 AC XY: 72157 AN XY: 74128

African (AFR) AF: 0.904 AC: 37036 AN: 40948

American (AMR) AF: 0.988 AC: 15093 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.992 AC: 3445 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5170 AN: 5170

South Asian (SAS) AF: 0.998 AC: 4811 AN: 4820

European-Finnish (FIN) AF: 1.00 AC: 10593 AN: 10594

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67979 AN: 68028

Other (OTH) AF: 0.977 AC: 2066 AN: 2114

Alfa AF: 0.703 Hom.: 2595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.32
DANN	Benign	0.37
PhyloP100		-1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs207524; hg19: chr21-25186489;